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- PDB-8wey: PSI-LHCI of the red alga Cyanidium caldarium RK-1 (NIES-2137) -

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Basic information

Entry
Database: PDB / ID: 8wey
TitlePSI-LHCI of the red alga Cyanidium caldarium RK-1 (NIES-2137)
Components
  • (Photosystem I ...) x 12
  • Lhcr1
  • Lhcr2
  • Lhcr3
KeywordsPHOTOSYNTHESIS / Photosystem I / ELECTRON TRANSPORT
Function / homology: / BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Unknown ligand
Function and homology information
Biological speciesCyanidium caldarium (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.92 Å
AuthorsKato, K. / Hamaguchi, T. / Nakajima, Y. / Kawakami, K. / Yonekura, K. / Shen, J.R. / Nagao, R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: The structure of PSI-LHCI from provides evolutionary insights into conservation and diversity of red-lineage LHCs.
Authors: Koji Kato / Tasuku Hamaguchi / Minoru Kumazawa / Yoshiki Nakajima / Kentaro Ifuku / Shunsuke Hirooka / Yuu Hirose / Shin-Ya Miyagishima / Takehiro Suzuki / Keisuke Kawakami / Naoshi Dohmae / ...Authors: Koji Kato / Tasuku Hamaguchi / Minoru Kumazawa / Yoshiki Nakajima / Kentaro Ifuku / Shunsuke Hirooka / Yuu Hirose / Shin-Ya Miyagishima / Takehiro Suzuki / Keisuke Kawakami / Naoshi Dohmae / Koji Yonekura / Jian-Ren Shen / Ryo Nagao /
Abstract: Light-harvesting complexes (LHCs) are diversified among photosynthetic organisms, and the structure of the photosystem I-LHC (PSI-LHCI) supercomplex has been shown to be variable depending on the ...Light-harvesting complexes (LHCs) are diversified among photosynthetic organisms, and the structure of the photosystem I-LHC (PSI-LHCI) supercomplex has been shown to be variable depending on the species of organisms. However, the structural and evolutionary correlations of red-lineage LHCs are unknown. Here, we determined a 1.92-Å resolution cryoelectron microscopic structure of a PSI-LHCI supercomplex isolated from the red alga RK-1 (NIES-2137), which is an important taxon in the Cyanidiophyceae. We subsequently investigated the correlations of PSI-LHCIs from different organisms through structural comparisons and phylogenetic analysis. The PSI-LHCI structure obtained shows five LHCI subunits surrounding a PSI-monomer core. The five LHCIs are composed of two Lhcr1s, two Lhcr2s, and one Lhcr3. Phylogenetic analysis of LHCs bound to PSI in the red-lineage algae showed clear orthology of LHCs between and , whereas no orthologous relationships were found between Lhcr1-3 and LHCs in other red-lineage PSI-LHCI structures. These findings provide evolutionary insights into conservation and diversity of red-lineage LHCs associated with PSI.
History
DepositionSep 19, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 16, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.3Nov 27, 2024Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / em_admin / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.pdbx_stereo_config / _chem_comp_bond.value_order / _em_admin.last_update / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2
C: Photosystem I iron-sulfur center
D: Photosystem I reaction center subunit II
E: Photosystem I reaction center subunit IV
F: Photosystem I reaction center subunit III
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit X
L: Photosystem I reaction center subunit XI
M: Photosystem I reaction center subunit XII
O: Photosystem I subunit O
1: Lhcr1
2: Lhcr2
3: Lhcr3
4: Lhcr1
5: Lhcr2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)557,226255
Polymers387,15817
Non-polymers170,068238
Water10,088560
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Photosystem I ... , 12 types, 12 molecules ABCDEFIJKLMO

#1: Protein Photosystem I P700 chlorophyll a apoprotein A1


Mass: 82698.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote)
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2


Mass: 82160.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote)
#3: Protein Photosystem I iron-sulfur center


Mass: 8822.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote)
#4: Protein Photosystem I reaction center subunit II


Mass: 15709.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote)
#5: Protein Photosystem I reaction center subunit IV


Mass: 6974.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote)
#6: Protein Photosystem I reaction center subunit III


Mass: 20520.506 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote)
#7: Protein/peptide Photosystem I reaction center subunit VIII


Mass: 3408.183 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote)
#8: Protein/peptide Photosystem I reaction center subunit IX


Mass: 4426.245 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote)
#9: Protein Photosystem I reaction center subunit X


Mass: 7105.433 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote)
#10: Protein Photosystem I reaction center subunit XI


Mass: 15343.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote)
#11: Protein/peptide Photosystem I reaction center subunit XII


Mass: 3010.698 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote)
#12: Protein Photosystem I subunit O


Mass: 16661.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote)

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Protein , 3 types, 5 molecules 14253

#13: Protein Lhcr1


Mass: 24117.104 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote)
#14: Protein Lhcr2


Mass: 24128.066 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote)
#15: Protein Lhcr3


Mass: 23826.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote)

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Sugars , 2 types, 8 molecules

#22: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#24: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 9 types, 790 molecules

#16: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER


Mass: 893.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#17: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 153 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#18: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


Mass: 450.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O2
#19: Chemical ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#20: Chemical
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C40H56
#21: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#23: Chemical...
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 25 / Source method: obtained synthetically
#25: Chemical...
ChemComp-5X6 / Zeaxanthin / (1R)-4-[(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4R)-4-hydroxy-2,6,6-trimethylcyclohexen-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaenyl]-3,5,5-trimethylcyclohex-3-en-1-ol


Mass: 568.871 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C40H56O2
#26: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 560 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: PSI-LHCI / Type: COMPLEX / Entity ID: #1-#15 / Source: NATURAL
Molecular weightValue: 0.55 MDa / Experimental value: NO
Source (natural)Organism: Cyanidium caldarium (eukaryote)
Buffer solutionpH: 6.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMMESMES-NaOH1
20.03 %DDMDDM1
SpecimenConc.: 2.83 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid mesh size: 200 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 39.8 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
4CTFFIND4.1CTF correction
7UCSF Chimera1.12model fitting
9RELION3.1initial Euler assignment
10RELION3.1final Euler assignment
11RELION3.1classification
12RELION3.13D reconstruction
13Servalcat0.2.0model refinement
14PHENIX1.18.2-3874model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 1.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 228449 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: RECIPROCAL
Atomic model buildingDetails: homology model / Source name: Other / Type: in silico model

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